Following the Whale Probe incident (in which Kirk and his crew saved the planet), the President and the Council agreed to drop all but one of the charges against the Enterprise crew, the remaining charge simply resulting in Kirk being demoted to captain – as he wanted all along – in gratitude for their service to Earth and the Federation. (Star Trek IV: The Voyage Home)

A short time later, Starfleet ColonelWest proposed a military offensive (code-named Operation Retrieve) aimed at invading Klingon space and rescuing the "hostages", Kirk and McCoy. Although West was confident that the prisoners could be retrieved, the President rejected his plan because of the probability that such an act would cause a full-scale war.

In 2372, fears of Changeling infiltration of the Federation government reached a high point when Dominion agents were discovered to have detonated a bomb at a diplomatic conference between the Federation and the Romulan Star Empire in Antwerp. Starfleet Admiral and Chief of Starfleet OperationsLeyton and Captain Benjamin Sisko advocated increased security on Earth following the bombing, and when the planetary power grid was disabled, Inyo declared martial law on the capital planet. Later, it was discovered that the grid had been disabled by Leyton's own agents, and that Leyton was leading an attempted military coup d'etat against the Federation civilian government. Leyton's coup was thwarted by Sisko, but as a result of the scandal, Jaresh-Inyo's political career ended. (DS9: "Homefront", "Paradise Lost")

The novel Articles of the Federation establishes that Jaresh-Inyo was elected in 2368 and defeated for re-election by Bolian Councillor Min Zife shortly after Leyton's attempted takeover. He died in May of 2380, being remembered as a great "peace-time president" being credited with the expansion of civil rights for sentient beings, and the opening of diplomatic relations with the Children of Tama, but not one suited for the job when war with the Dominion became inevitable.

The method of electing the President of the United Federation of Planets has never been discussed in a canonical Star Trek production. The Last Unicorn sourcebook for the Federation suggests that the President is elected by members of the Federation Council, similar to a parliamentary government.

Answering questions as to why Jaresh-Inyo put Earth into a state of emergency, Ronald D. Moore stated:

"We wanted to tell the story of an attempted military coup of the Federation and that meant dealing with the Fed president. However, that meant the troops "in the streets" had to be on Earth and that Earth itself had to be under martial law since the Fed is headquartered on Earth. We discussed having the Prez "federalize" the Earth defense forces or supersede the authority of an indigenous Earth Govt, but the story kept getting too complicated and we didn't want to start mentioning all these other players and organizations that we weren't going to see. So in the end, we skirted the issue of who actually governs Earth. Personally, I think there is an Earth Govt that operates like more powerful versions of States do in the US system, but this is all VERY murky water." (AOL chat,1997)

The President of the Federation and the duties of the office are the subjects of the novel Articles of the Federation, which tells the story of a year in the life of the newly-elected Federation President in a style similar to that of the television series The West Wing. The novel also names several prior Federation Presidents, including the ones who are canonically "name unknown." It establishes that the office is held in four-year terms (without a two-term limit), similar to the modern American presidency.

The novel A Time for War, A Time for Peace establishes that an individual anonymously submits an application for candidacy to the Federation Council, which reviews each application and certifies that a candidate fills all qualifications for the office. Approved candidates then campaign in a popular election. All Federation citizens within and without UFP territory are allowed to submit their ballots, which are tabulated over the course of a week by two independent auditing firms and by the Federation government before a winner is certified. The Federation News Service commonly projects a winner in the days leading up to Election Day, and has never projected erroneously.

Canonical and non-canonical Presidents of the United Federation of Planets depicted in the television series, films, novels, and comics include:

2285-2288: Hiram Roth (Human male) (Star Trek IV: The Voyage Home, dates of at least one term and name from Articles of the Federation by Keith R.A. DeCandido)

2289-2300: Ra-ghoratreii (Efrosian male) (Star Trek VI: The Undiscovered Country", dates from Articles of the Federation by Keith R.A. DeCandido, species name from Star Trek production office name for makeup design, character name from novelization of Star Trek VI: The Undiscovered Country by J.M. Dillard)

Post 2320 (dates unestablished): Hikaru Sulu (Human Male) (The Return by William Shatner) (Note: The Return establishes President Sulu to have been the Federation's only three-term president, but the later novel Articles of the Federation contradicts the idea that there had been no prior three-term presidents by establishing Ra-ghoratreii to have served three terms. There is no reference to Sulu becoming Federation President in any other novels, creating the possibility that Sulu only becomes President in the so-called "Shatnerverse" continuity.) All that is mentioned in other works is that Sulu retained his position as captain of the Excelsior until at least 2320.